GolP: An atomistic force‐field to describe the interaction of proteins with Au(111) surfaces in water

Iori, Federico; Felice, Rosa Di; Molinari, Elisa; Corni, Stefano

doi:10.1002/jcc.21165

Cited by 250 publications

(442 citation statements)

References 86 publications

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“…Notable examples of calculations of this kind are works on Cys-Au(111) interactions (Buimaga-Iarinca & Calborean, 2012;Di Felice et al 2003;Di Felice & Selloni, 2004;Fajín et al 2013;Nazmutdinov et al 2007), often used for protein immobilization (Vigmond et al 1994). Static DFT calculations on amino acids or simpler molecules representative of chemical groups in natural amino acids on metals (Hong et al 2009;Iori et al , 2009) have also highlighted the peculiar nature of the amino acid-metal interaction. Depending on the partners, such an interaction ranges from clear non-bonding (e.g.…”

Section: Morphologymentioning

confidence: 99%

“…However, many of these FFs fall short in reproducing the properties of protein-inorganic surface systems. To alleviate this problem, many useful models Kokh et al 2010) and FF parameters (De la Torre et al 2009;Heinz et al 2013;Iori et al 2009;Schneider & Colombi Ciacchi, 2010;Wright et al 2013a) for material surfaces have been introduced that have been designed to be compatible with FFs for biomolecular systems. These FFs are still rather young and their improvement is an area of active research.…”

Section: Introductionmentioning

confidence: 99%

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Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

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Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

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Section: Morphologymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

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“…11 We used the AMBER GAFF (Version 1.7, Nov 2013) for polymers, and the TIP3P model for water molecules. Additionally, the values in Table 5 of ref 12 were used for the van der Waals (vdW) parameters for Au, and the other Au-related parameters were prepared using the DFT calculations. We first minimized the energy of the water molecules for 5000 steps and then minimized the energy of entire model systems for 5000 steps.…”

mentioning

confidence: 99%

Theoretical Investigation for Heterojunction Effects in Polymer-stabilized Au Nanocluster Catalysis: Difference in Catalytic Activity between Au:PVP and Au:PAA

et al. 2016

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To elucidate the differences in the catalytic activities of two different polymer-stabilized Au cluster catalysts, Au:PVP and Au:PAA in the aerobic oxidation of p-hydroxybenzyl alcohol, the characteristics of these two kinds of polymer-stabilized Au nanocluster (Au NC) catalysts were investigated theoretically. The results of DFT and MD calculations showed that the coordination structures of the polymers onto the Au cluster play an important role for this difference. 68 In order to elucidate the catalytic activity of Au:PVP catalysts, we had performed hybrid density functional theory (DFT) calculations for the Au:PVP model systems, 9 which showed that electron donation from the adsorbed model PVP molecules (ethylpyrrolidone; EP) to Au 13 produces negatively charged O 2 on the Au 13 -EP 4 model system. These results suggest that PVP acts as not only a stabilizer but also an electron donor to Au clusters.Additionally, Tsukuda et al. reported that the Au NCs stabilized by poly(allylamine) [PAA; (C 3 H 5 NH 3 ) n ], abbreviated as Au:PAA, can also selectively oxidize p-hydroxybenzyl alcohol to the corresponding aldehyde under the same conditions; however, its activity is much lower than that of Au:PVP.7 At present, little is known about the reason for this difference in the catalytic activity between Au:PVP and Au:PAA. To elucidate this difference, the characteristics of these two types of polymerstabilized Au NC catalysts were investigated using DFT and molecular dynamics (MD) calculations.To examine the heterojunction effect between the polymer model molecules and Au NCs, DFT calculations were performed using B3LYP functional. The scalar relativistic effective core potential (ECP) with double-zeta basis sets (LANL2DZ) for all gold atoms and 6-31G 1, 2, 3) were used as the model systems investigated. EP and PA were used for the model compounds for PVP and PAA, respectively, because it was difficult to theoretically deal with real polymers. All the geometries for the model systems were fully optimized except for the O 2 -adsorbed models, in which the structure of the Au 13 -EPs or the Au 13 -PAs moiety was fixed and the position of the adsorbed O 2 molecule was optimized. For these calculations, Gaussian09 program suite was used. 10All MD simulations were performed by AMBER 14 program. 11 We used the AMBER GAFF (Version 1.7, Nov 2013) for polymers, and the TIP3P model for water molecules. Additionally, the values in Table 5 of ref 12 were used for the van der Waals (vdW) parameters for Au, and the other Au-related parameters were prepared using the DFT calculations. We first minimized the energy of the water molecules for 5000 steps and then minimized the energy of entire model systems for 5000 steps. Next, we raised the temperature of the model systems to 300 K under NTP conditions to obtain the equilibrium states. Finally, we performed replica exchange molecular dynamics (REMD) 13 simulations for the model system under NVT condition for 4 ns, with temperatures ranging from 294 to 441 K for the Au 55 :PVP, fro...

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“…47 Moreover, a relatively parallel orientation of catechol to the gold surface attributed to p binding is also consistent with previous results. 9,21 The binding energies between organic molecules and the gold surface are computed following the procedure of the GolP force field, in which Lennard-Jones …”

Section: A Single Molecule Adsorptionmentioning

confidence: 99%

Molecular dynamics simulation of a DOPA/ST monolayer on the Au(111) surface

Kong

Peters

With

et al. 2013

Phys. Chem. Chem. Phys.

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aIn order to study the influence of molecular structure on the formation of a monolayer, two molecules have been considered, namely N-stearoyldopamine (DOPA) and 4-stearyl-catechol (ST). The difference between these two molecules is the amide group in DOPA. By investigating these monolayers at different surface areas per molecule, the molecular configurations of a DOPA/ST monolayer on the Au(111) surface were obtained. We conclude that for both kinds of molecules, the p-interaction between the catechol group and the Au(111) surface is important. Compared to experimental results, the catechol groups are found either parallel or perpendicular to the Au(111) surface in MD simulation.The difference between DOPA and ST systems is that when there are fewer molecules on the Au (111) surface, in the DOPA system, the amount of catechol groups perpendicular with their hydroxyls orienting towards the surface is less than that of the ST system. Further analysis of catechol groups and amide groups indicates that various kinds of hydrogen bonds formed in the DOPA system have a profound influence on the structure and regularity of the monolayer.

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GolP: An atomistic force‐field to describe the interaction of proteins with Au(111) surfaces in water

Cited by 250 publications

References 86 publications

Modeling and simulation of protein–surface interactions: achievements and challenges

Modeling and simulation of protein–surface interactions: achievements and challenges

Theoretical Investigation for Heterojunction Effects in Polymer-stabilized Au Nanocluster Catalysis: Difference in Catalytic Activity between Au:PVP and Au:PAA

Molecular dynamics simulation of a DOPA/ST monolayer on the Au(111) surface

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